Engineering:TCON 09 08 2005

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Expected Core 3 Attendees: Andy Saykin(Dartmouth), Martina Panzenboeck (UCI), Jim Fallon (UCI), Jessica Turner (UCI)

Agenda:

Introduction (Ron)
Engineering Progress (30 min) (Note: details for this are available in a wiki page here and a consolidated powerpoint is available here)
- (15 min) Application Projects from Programming Week and more ...(Steve Pieper)
- (15 min) Algorithms and Infrastructure Projects from Programming Week (Bill Lorensen)
(15 min) Core 3 response to projects content and future direction
(10 min) Core 3 suggestions for items for discussion in Boston on September 26th

Minutes

Core 1 and Core 2 meet and split into small teams
Setup Sandbox for shared efforts
Tina Kapur organized reports
Ron was pleased with interactions between Cores
Move some emphasis from Core 1 to Core 3 by the Engineering team
- All-hands meeting marks 1/2 time for Core 3, time to start writing papers

Structural, Functional and Diffussion Imaging were focus
Main focus has been diffusion
Quantative Fiber Tracking Project
- Define quantaties, i.e. fa and ensure consistent implementation
- Unify into ITK, first instance is clustering using Normalized Cuts
- Basic algorithm
  - Generate large numbers of tracks
  - Have the algorithm identify a specified numbers of similar tracks via Normalized Cuts
DLPFC Semi-automatic Segmentor
- Baysen classifier, and rules to segment the dorsal-lateral prefrontal cortex
- Slicer workflow has been defined
- Rules have been identified for other structures, and new structures should be added soon
EPI to structural image registration
- Use non-rigid registration ITK tools to address this problem
- Used notion of image orientations to address different acquisition orientations
- Resulted in better ITK support for orientation, useful in clinical settings
- Rigid and Affine registration done, exposed in Slicer
- Soon Demon's and B-Spline based registrations
- Need to compare to existing tools: SPM and FSL
Some of this work has been published in the Insight Journal

Spherical harmonics added to ITK
Database and mechanisms to gather statistics on populations from many different sources
- Much of the infrastructure exists inside Dart
Bayesian Classifier / edge-preserving affine invariant noise remover algorithm
- Transition from Matlab to ITK
3d adaptive tetrahedral meshing
- Generate computational stable solid meshes for deformable registration
- Transition algorithms to ITK
2d/3d landmark detection algorithm
- Look for corners in the brain, may be useful for registration tasks
Flux diffusion algorithm
- Port anisotropic diffusion algorithm for thin structures to ITK
Intensity correction algorithm
- Port external code to ITK, promote to first class filter

ITKu
- Expose ITK functions at the commandline
- Suitable for batch tasks
Grid adaption for NAMIC algorithms
- LONI pipeline and Condor job submission
NrrdIO Image format
- Support for DTI-type structures in files
- Handle measurement frames for tensors, variable length vectors
DTMRI Nightly Testing
- Nightly regression tests for DTMRI Slicer module
LONI Pipeline for UNC shape analysis
- Adapt UNC scripts to LONI Pipeline
Slicer 3.0 Architecture Meeting
- Still in dream/planning stage
- Need significant input from Core 3
- May be completely different from existing Slicer implementation
- What is useful from all available technologies? How do we take best-of-breed
- Need to provide architectural support to preserve algorithm development investments
ITK Release (2.2)
- Much has been added at the behest of NAMIC

Andy: development is really exciting from a Core 3 perspective
- Tools need to migrate into Core 3 day-to-day use
Some must-haves are already recorded and will be presented in Boston on Sept 26th.
Bill Lorensen invited Core 3 to participate in future tcons